75bb2c814a
Added addObservations-related methods to multivariate TE calculators.
...
This is needed to implement auto-embedding methods later.
2018-02-25 18:54:36 +00:00
b0fc309d6a
Add overloadings for 1d continuous variables in KSG mixed calc.
2018-01-12 22:22:46 +00:00
0278f95ae9
Enabled use of USE_GPU property for KSG calculators in the AutoAnalysers for CMI, TE, CTE and AIS
2017-12-30 12:03:17 +11:00
64f1142b40
Added argument to choose which variable to reorder in GPU CMI code.
2017-12-19 20:42:58 +00:00
65ac0e9ff8
Removed unnecesary overloaded method in KSG CMI calc.
2017-12-19 20:41:11 +00:00
2f1cd192b8
Fixed small typo in Java KSG CMI calculator.
2017-12-18 17:50:37 +00:00
d0304ae0c4
Added Java-side JNI functions and ensureKdTreesConstructed to KSG CMI.
2017-12-12 11:19:40 +00:00
f4ca442de4
Now KSG MI calc does not build KdTrees if GPU is going to be used.
2017-12-12 11:10:50 +00:00
d010f32635
Updated getProperty and removed spurious dependency in KSG MI calc.
2017-12-12 11:04:32 +00:00
eabd7f3701
Fixed typo in Kozachenko entropy calculator.
2017-11-28 16:58:13 +00:00
444fb70801
Added addObservations-type functions to Kozachenko entropy calculator.
2017-11-28 16:56:51 +00:00
e290040d8d
Added docs to Kozachenko entropy calculator.
2017-11-28 16:26:46 +00:00
35df6ca3da
Kozachenko entropy estimator now adds noise to data by default.
2017-11-28 16:04:09 +00:00
9c96ceb850
Fixed logic for when parameter values (in particular auto-embedded properties) are written back into the properties table after the calculation. This was happening only when we had the "all pairs" option selection, when it should only happen when this is not selected.
2017-11-28 12:36:06 +11:00
589d51674e
Altering the escaped data filename in AutoAnalyser to be properly escaped using non-regex replace, and also rolling back the use of escaping to only Java (Matlab and Python on windows seem fine with the non-escaped filenames, for e.g. the paths earlier in the generated code)
2017-11-27 10:19:36 +11:00
3bfbaa7ad3
In AutoAnalyser escaping data filenames when they are written to the generated code. This is important for windows filenames. Am not sure why it didn't come up before as an issue though.
2017-11-27 09:57:07 +11:00
61f4bf3276
Adding getProperty lines to handle USE_GPU property for KSG MI calculator
2017-11-27 09:26:19 +11:00
db0503d763
Having AutoAnalyser continue with the calculation where the generated code cannot be written
2017-11-26 18:04:29 +11:00
df8724b872
Altered AutoAnalyserLauncher to either auto-detect jar location or assume demos/AutoAnalyser folder is current location (if a command line argument is given). Similarly, altered AutoAnalyser to either take location of demos/AutoAnalyser folder, or assume it is the current folder.
2017-11-26 01:10:30 +11:00
fd804d0d0c
Added properties for running GPU calculation to MI AutoAnalyser
2017-11-26 01:07:19 +11:00
69af7252cd
Added debug print on working directory to AutoAnalyser startup
2017-11-25 00:15:37 +11:00
ddf3b4de0a
Moving AutoAnalyser java files into the main source location rather than in the demos location. This commit includes the moving of the files themselves. Further commits will alter the ant script and run scripts to have correct classpath, etc.
2017-11-24 21:07:33 +11:00
142fbb4541
Merge branch 'master' of github.com:jlizier/jidt
...
Merging in Pedro's mixed Kraskov changes, plus further work on GPU for Kraskov MI
2017-11-24 15:30:20 +11:00
9e77ebdadf
Tweak to method to print out an array of ints
2017-11-22 20:49:05 +11:00
1bb67f0840
Adding neighbour search utilities in preparation for attempting fast surrogate generation (performing multiple neighbour searches at once where we can); in particular adding a countPointsWithinR with a remapping of the point's indices. Unit test added as well for this.
2017-11-22 20:48:30 +11:00
446ac4ae59
Merge branch 'master' into gpu
2017-11-21 14:58:15 +00:00
c5c38335ef
Merge pull request #58 from pmediano/master
...
Major improvements to KSG mixed (continuous-discrete) MI calculator.
2017-11-22 00:23:10 +11:00
ecda70f8e9
Hard-setting dynCorrExclTime to 0 in KSG mixed calc.
...
Previous implementation was incomplete due to a mismatch between the
sample indices in the full and marginal KdTrees. Some code has been left
to guide future development.
2017-11-20 14:47:00 +00:00
25df49fa5a
KSG mixed calc now allocates memory for locals only if requested.
2017-11-20 14:26:25 +00:00
8f169171e1
Fixed small bug in KSG mixed calc surrogates.
...
Surrogate calculator was applying timeDiff twice, so surrogate
dataset had abs(timeDiff) less observations than it should.
2017-11-20 14:14:49 +00:00
d40024e1cd
Allow negative timeDiff in KSG mixed calc.
2017-11-20 14:02:00 +00:00
0e27dbcbc2
Fixed default value of dynamic exclusion window in Kernel MI calculator to be 0. Technically it is zero (because dynCorrExcl boolean is set to false, but gets reported as 100 because the integer value of dynCorrExclTime was not set to 0 itself)
2017-09-02 20:18:36 +10:00
ed71502bc2
Remove old cudaLibraryLoad code and unnecessary dependencies.
2017-08-31 16:22:12 +01:00
83e77e8b3a
Merge Joe's master into Pedro's master with KSG mixed changes.
2017-08-30 17:36:32 +01:00
f56ac6e69e
Fix bug with Theiler window in KSG mixed calc.
2017-08-30 13:30:30 +01:00
5961fb6246
Add Theiler window and jitter to KSG mixed calc.
2017-08-30 12:17:02 +01:00
d36c803e41
Added utilities to convert between estimate values and p-values for an analytic null distribution in bulk (array calls)
2017-08-30 16:24:17 +10:00
626293b84d
More docs for KSG mixed calc.
2017-08-30 01:19:54 +01:00
e11218631e
Added myself as author of KSG mixed calculator.
2017-08-29 23:56:28 +01:00
49afa343fc
Removed old variables and functions from KSG mixed, added docs.
2017-08-29 23:55:10 +01:00
19f2c5abbc
Performance tweaks for TE Discrete, which should make a difference when the state space is large in comparison to the number of samples.
2017-08-28 00:36:24 +10:00
c59d932a44
Misc spacing/comment patches
2017-08-23 00:19:43 +10:00
b2e3ae1ca0
Added missing getProperty() method to Conditional TE calculator Kraskov
2017-08-23 00:19:09 +10:00
0e40ec2401
Initialising conditional TE calculator to have one conditional dimension by default instead of none. Also fixing the way the conditional parameters are printed via getProperty() when they are null.
2017-08-23 00:18:41 +10:00
4db008ce33
For Conditional MI calculators (sontinuous), adding setObservations and addObservations method signatures which take univariate arrays (only work if initialised dimensionalities are univariate) into the interface, and the common base class. This is in preparation for the CMI AutoAnalyser
2017-08-22 21:26:44 +10:00
4d6fc1a572
Updated Kozachenko-Leonenko multivariate Entropy calculator to implement EntropyCalculator interface, in preparation for Entropy AutoAnalyser
2017-08-21 14:56:20 +10:00
086bee5945
Making continuous MultiInfoCalculator classes implement the InfoMeasureCalculatorContinuous interface. For the interfaces, this means removing methods where duplicated. For implementing classes, this means adding the missing methods.
2017-08-18 23:42:43 +10:00
057f17e338
Making continuous PredictiveInfoCalculator classes implement the InfoMeasureCalculatorContinuous interface. For the interfaces, this means removing methods where duplicated. And fixed the common implementing class to have the missing getProperty method.
2017-08-18 23:11:37 +10:00
65c7cd99cc
Making continuous EntropyCalculator and EntropyCalculatorMultiVariate classes implement the InfoMeasureCalculatorContinuous interface. For the interfaces, this means removing methods where duplicated. Also added NUM_DIMENSIONS property to EntropyCalculatorMultiVariate interface, so that these calculators can have an initialise() method which takes no parameters. Fixed all implementing classes to have any methods that they were missing.
2017-08-18 20:18:29 +10:00
d6bd16546b
Added new interface InfoMeasureCalculatorContinuous to capture common methods for continuous calculators. Also adapted most continuous calculators to implement this, which involved in many cases removing duplicate definitions of these methods in the interfaces for these measures. For ConditionalMI calculator, this meant we needed to add an implementation of the zero-argument initialise() call also. Still need to do MultiInfo, PredictiveInfo and Entropy in future, as they're missing a few methods.
2017-08-18 16:54:55 +10:00
Pedro Martinez Mediano